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Merged
leopoldguyot merged 3 commits into from
Jun 9, 2026
Merged

Issue 71 #97

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bf154d9
first tentative is missing operator
leopoldguyot Jun 8, 2026
dbbe129
improve is missing filter plotting
leopoldguyot Jun 9, 2026
0ecbc3d
address comments
leopoldguyot Jun 9, 2026
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40 changes: 34 additions & 6 deletions R/code_generator_processQFeatures.R
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Original file line number Diff line number Diff line change
Expand Up @@ -369,19 +369,33 @@ codeGeneratorFiltering <- function(qf, condition, type, step_number) {
for (i in 1:length(condition)) {
annotation <- as_r_string_literal(condition[[i]]$annotation)
if (condition[[i]]$annotation == ".qfeaturesgui_rowname") {
if (condition[[i]]$operator == "==") {
if (is_missingness_filter_operator(condition[[i]]$operator)) {
build_condition <- if (condition[[i]]$operator == "is_missing") {
"is.na(rownames(rowData(se)))"
} else {
"!is.na(rownames(rowData(se)))"
}
vector <- ""
} else if (condition[[i]]$operator == "==") {
build_condition <- paste0("rownames(rowData(se)) %in% ")
vector <- as_r_vector_literal(condition[[i]]$value)
} else {
build_condition <- paste0("!(rownames(rowData(se)) %in% ")
vector <- paste0(as_r_vector_literal(condition[[i]]$value), ")")
}
} else {
if (condition[[i]]$operator == "==") {
if (is_missingness_filter_operator(condition[[i]]$operator)) {
build_condition <- if (condition[[i]]$operator == "is_missing") {
paste0("is.na(rowData(se)[[", annotation, "]])")
} else {
paste0("!is.na(rowData(se)[[", annotation, "]])")
}
vector <- ""
} else if (condition[[i]]$operator == "==") {
build_condition <- paste0("rowData(se)[[", annotation, "]] %in% ")
vector <- as_r_vector_literal(condition[[i]]$value)
} else if (condition[[i]]$operator == "!=") {
build_condition <- paste0("!(rowData(se)[[", annotation, "]] %in% ")
build_condition <- paste0("!is.na(rowData(se)[[", annotation, "]]) & !(rowData(se)[[", annotation, "]] %in% ")
vector <- paste0(as_r_vector_literal(condition[[i]]$value), ")")
} else {
build_condition <- paste0("rowData(se)[[", annotation, "]] ", condition[[i]]$operator, " ")
Expand Down Expand Up @@ -418,19 +432,33 @@ for(i in 1:length(step%s_setNames)){
for (i in 1:length(condition)) {
annotation <- as_r_string_literal(condition[[i]]$annotation)
if (condition[[i]]$annotation == ".qfeaturesgui_rowname") {
if (condition[[i]]$operator == "==") {
if (is_missingness_filter_operator(condition[[i]]$operator)) {
build_condition <- if (condition[[i]]$operator == "is_missing") {
"is.na(rownames(colData(se)))"
} else {
"!is.na(rownames(colData(se)))"
}
vector <- ""
} else if (condition[[i]]$operator == "==") {
build_condition <- paste0("rownames(colData(se)) %in% ")
vector <- as_r_vector_literal(condition[[i]]$value)
} else {
build_condition <- paste0("!(rownames(colData(se)) %in% ")
vector <- paste0(as_r_vector_literal(condition[[i]]$value), ")")
}
} else {
if (condition[[i]]$operator == "==") {
if (is_missingness_filter_operator(condition[[i]]$operator)) {
build_condition <- if (condition[[i]]$operator == "is_missing") {
paste0("is.na(colData(se)[[", annotation, "]])")
} else {
paste0("!is.na(colData(se)[[", annotation, "]])")
}
vector <- ""
} else if (condition[[i]]$operator == "==") {
build_condition <- paste0("colData(se)[[", annotation, "]] %in% ")
vector <- as_r_vector_literal(condition[[i]]$value)
} else if (condition[[i]]$operator == "!=") {
build_condition <- paste0("!(colData(se)[[", annotation, "]] %in% ")
build_condition <- paste0("!is.na(colData(se)[[", annotation, "]]) & !(colData(se)[[", annotation, "]] %in% ")
vector <- paste0(as_r_vector_literal(condition[[i]]$value), ")")
} else {
build_condition <- paste0("colData(se)[[", annotation, "]] ", condition[[i]]$operator, " ")
Expand Down
139 changes: 135 additions & 4 deletions R/server_module_filtering_box.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,19 +24,25 @@ server_module_filtering_box <- function(id, assays_to_process, type, state) {
">" = "is greater than",
">=" = "is greater than or equal to",
"==" = "is equal to",
"!=" = "is not equal to"
"!=" = "is not equal to",
"is_missing" = "is missing",
"is_not_missing" = "is not missing"
)
operator_choices_all <- c(
"Less than" = "<",
"Less than or equal to" = "<=",
"Greater than" = ">",
"Greater than or equal to" = ">=",
"Equal to" = "==",
"Not equal to" = "!="
"Not equal to" = "!=",
"Is missing" = "is_missing",
"Is not missing" = "is_not_missing"
)
operator_choices_categorical <- c(
"Equal to" = "==",
"Not equal to" = "!="
"Not equal to" = "!=",
"Is missing" = "is_missing",
"Is not missing" = "is_not_missing"
)

combined_samples_annotations <- reactive({
Expand Down Expand Up @@ -142,6 +148,9 @@ server_module_filtering_box <- function(id, assays_to_process, type, state) {
req(input$filter_operator)
is_categorical <- annotations_type() %in% c("character", "factor")
is_equality_operator <- input$filter_operator %in% c("==", "!=")
if (is_missingness_filter_operator(input$filter_operator)) {
return(FALSE)
}
if (!(is_categorical && is_equality_operator)) {
return(FALSE)
}
Expand All @@ -154,6 +163,10 @@ server_module_filtering_box <- function(id, assays_to_process, type, state) {
if (is.null(state_filter_value) && !is.null(state)) {
state_filter_value <- state$filter_value
}
req(input$filter_operator)
if (is_missingness_filter_operator(input$filter_operator)) {
return(NULL)
}
is_categorical <- annotations_type() %in% c("character", "factor")
is_equality_operator <- input$filter_operator %in% c("==", "!=")
if (is_categorical) {
Expand Down Expand Up @@ -204,6 +217,9 @@ server_module_filtering_box <- function(id, assays_to_process, type, state) {
req(input$annotation_selection)
req(input$filter_operator)
req(annotations_type())
if (is_missingness_filter_operator(input$filter_operator)) {
return()
}
is_categorical <- annotations_type() %in% c("character", "factor")
if (!is_categorical) {
return()
Expand Down Expand Up @@ -271,6 +287,12 @@ server_module_filtering_box <- function(id, assays_to_process, type, state) {
} else {
input$annotation_selection
}
if (is_missingness_filter_operator(input$filter_operator)) {
return(paste(
annotation_label,
operator_labels[[input$filter_operator]]
))
}
if (annotations_type() %in% c("character", "factor") &&
input$filter_operator %in% c("==", "!=")) {
selected_values <- as.character(input[[paste0("filter_ui_", type)]])
Expand Down Expand Up @@ -299,6 +321,13 @@ server_module_filtering_box <- function(id, assays_to_process, type, state) {
req(input$annotation_selection)
req(input$filter_operator)
req(input$filter_operator %in% names(operator_labels))
if (is_missingness_filter_operator(input$filter_operator)) {
return(list(
annotation = input$annotation_selection,
operator = input$filter_operator,
value = NULL
))
}
filter_value <- input[[paste0("filter_ui_", type)]]
if (is.null(filter_value) || is_empty_categorical_multiselect()) {
return(NULL)
Expand Down Expand Up @@ -386,6 +415,18 @@ server_module_annotation_plot <- function(
req(annotation_values())
selected_operator <- filter_operator()
req(selected_operator)
if (is_missingness_filter_operator(selected_operator)) {
condition_mask <- apply_filter_operator(
values = annotation_values(),
operator = selected_operator,
target = NULL
)
plot_values <- missingness_filter_plot_values(
values = annotation_values(),
operator = selected_operator
)
return(plot_values[condition_mask])
}
condition_mask <- apply_filter_operator(
values = annotation_values(),
operator = selected_operator,
Expand All @@ -395,7 +436,16 @@ server_module_annotation_plot <- function(
annotation_values()[condition_mask]
})
output$plot <- renderPlotly({
annotation <- annotation_values()
selected_operator <- filter_operator()
req(selected_operator)
if (is_missingness_filter_operator(selected_operator)) {
annotation <- missingness_filter_plot_values(
values = annotation_values(),
operator = selected_operator
)
} else {
annotation <- annotation_values()
}
filtered <- filtered_annotation()
selected <- selected_annotation()

Expand All @@ -413,6 +463,21 @@ server_module_annotation_plot <- function(
} else {
selected
}
if (is_missingness_filter_operator(selected_operator)) {
operator_label <- if (selected_operator == "is_missing") {
"Is missing"
} else {
"Is not missing"
}
return(error_handler(
missingness_annotation_plot_wrapper,
component_name = "annotation_plot (filtering_box)",
annotation = annotation,
filtered_annotation = filtered,
assay_name = plot_title,
annotation_name = paste0(operator_label, " (", annotation_label, ")")
))
}

error_handler(
annotation_plot_wrapper,
Expand All @@ -426,6 +491,72 @@ server_module_annotation_plot <- function(
})
}

missingness_filter_plot_values <- function(values, operator) {
condition_mask <- apply_filter_operator(
values = values,
operator = operator,
target = NULL
)
if (operator == "is_missing") {
false_label <- "Is not missing"
true_label <- "Is missing"
} else if (operator == "is_not_missing") {
false_label <- "Is missing"
true_label <- "Is not missing"
} else {
stop(paste0("Unsupported missingness operator: ", operator))
}
factor(
ifelse(condition_mask, true_label, false_label),
levels = c(false_label, true_label)
)
}

missingness_annotation_plot_wrapper <- function(
annotation,
filtered_annotation,
assay_name,
annotation_name
) {
categories <- levels(annotation)
annotation <- factor(annotation, levels = categories)
before_counts <- as.integer(table(annotation))

plot <- plot_ly() %>%
plotly::add_trace(
x = categories,
y = before_counts,
type = "bar",
name = "Before Filtering"
) %>%
layout(
barmode = "group",
xaxis = list(title = paste0("Filter Result: ", annotation_name)),
yaxis = list(title = "Number of appearances"),
title = assay_name
) %>%
config(displaylogo = FALSE, toImageButtonOptions = list(
format = "svg",
filename = "annotation_plot",
height = 500,
width = 700,
scale = 1
))

if (length(filtered_annotation) > 0) {
filtered_annotation <- factor(filtered_annotation, levels = categories)
after_counts <- as.integer(table(filtered_annotation))
plot <- plot %>%
plotly::add_trace(
x = categories,
y = after_counts,
type = "bar",
name = "After Filtering"
)
}
plot
}

#' @title Annotation plot wrapper
#'
#' @param annotation_df A data.frame that contains the annotation values
Expand Down
22 changes: 21 additions & 1 deletion R/server_module_filtering_tab.R
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Original file line number Diff line number Diff line change
Expand Up @@ -151,6 +151,12 @@ server_module_filtering_tab <- function(
filtering_condition_specs[[paste0("condition_spec_", i)]]
})
specs <- Filter(function(spec) {
if (is.list(spec) &&
!is.null(spec$annotation) &&
!is.null(spec$operator) &&
is_missingness_filter_operator(spec$operator)) {
return(TRUE)
}
is.list(spec) &&
!is.null(spec$annotation) &&
!is.null(spec$operator) &&
Expand Down Expand Up @@ -326,6 +332,12 @@ feature_filtering <- function(qfeatures, condition_specs) {
#' @keywords internal
#'
apply_filter_operator <- function(values, operator, target) {
if (operator == "is_missing") {
return(is.na(values))
}
if (operator == "is_not_missing") {
return(!is.na(values))
}
if (length(target) == 0) {
return(rep(FALSE, length(values)))
}
Expand All @@ -334,7 +346,7 @@ apply_filter_operator <- function(values, operator, target) {
if (operator == "==") {
return(values %in% target_values)
}
return(!(values %in% target_values))
return(!is.na(values) & !(values %in% target_values))
}
operator_functions <- list(
"==" = `==`,
Expand All @@ -349,3 +361,11 @@ apply_filter_operator <- function(values, operator, target) {
}
operator_functions[[operator]](values, target)
}

missingness_filter_operators <- function() {
c("is_missing", "is_not_missing")
}

is_missingness_filter_operator <- function(operator) {
operator %in% missingness_filter_operators()
}
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